Sodium in PDB 5kdp: E491A Mutant of Choline Tma-Lyase

All present enzymatic activity of E491A Mutant of Choline Tma-Lyase:
4.3.99.4;

The structure of E491A Mutant of Choline Tma-Lyase, PDB code: 5kdp was solved by M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.47 / 1.90
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	228.922, 228.922, 78.924, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 24.4

The binding sites of Sodium atom in the E491A Mutant of Choline Tma-Lyase (pdb code 5kdp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the E491A Mutant of Choline Tma-Lyase, PDB code: 5kdp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the E491A Mutant of Choline Tma-Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E491A Mutant of Choline Tma-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:27.7 occ:1.00 O A:MET748 2.2 21.6 1.0 O A:HOH1525 2.3 26.6 1.0 O A:HOH1071 2.4 20.6 1.0 O A:HOH1370 2.4 20.0 1.0 O A:SER746 2.5 26.2 1.0 O A:HOH1537 2.7 31.2 1.0 HD22 A:ASN750 3.0 32.4 1.0 HA A:ALA749 3.2 27.2 1.0 C A:MET748 3.3 22.0 1.0 HA A:SER746 3.4 30.9 1.0 C A:SER746 3.4 25.6 1.0 H A:ASN750 3.5 27.6 1.0 ND2 A:ASN750 3.8 27.0 1.0 CA A:SER746 3.9 25.8 1.0 HD21 A:ASN750 4.0 32.4 1.0 CA A:ALA749 4.0 22.6 1.0 N A:ALA749 4.1 22.2 1.0 O A:HOH1524 4.2 32.0 1.0 N A:ASN750 4.2 23.0 1.0 O A:HOH1730 4.2 42.4 1.0 N A:MET748 4.2 23.6 1.0 O C:HOH1456 4.2 22.8 1.0 O A:LEU787 4.3 28.0 1.0 O A:HOH1072 4.3 40.8 1.0 HB2 A:SER746 4.3 29.9 1.0 H A:MET748 4.4 28.3 1.0 CA A:MET748 4.4 22.8 1.0 O A:VAL745 4.4 24.5 1.0 C A:LYS747 4.4 23.2 1.0 N A:LYS747 4.4 24.8 1.0 O C:HOH1271 4.6 33.2 1.0 HB2 A:ASN750 4.6 30.9 1.0 HA A:LYS747 4.6 28.2 1.0 O C:HOH1279 4.6 38.5 1.0 C A:ALA749 4.7 23.0 1.0 O A:GLY788 4.7 20.7 1.0 HE3 C:LYS439 4.7 60.2 1.0 HZ1 C:LYS439 4.7 60.3 1.0 CB A:SER746 4.7 24.9 1.0 CA A:LYS747 4.8 23.5 1.0 OD1 A:ASN789 4.8 23.1 1.0 O A:LYS747 4.9 23.9 1.0 H A:ALA749 4.9 26.7 1.0 CG A:ASN750 4.9 27.7 1.0 HB2 A:MET748 4.9 27.2 1.0

Sodium binding site 2 out of 2 in the E491A Mutant of Choline Tma-Lyase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E491A Mutant of Choline Tma-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na901 b:33.7 occ:1.00 O C:MET748 2.2 24.9 1.0 O C:HOH1386 2.3 30.9 1.0 O C:HOH1525 2.3 32.8 1.0 O C:SER746 2.4 28.3 1.0 O A:HOH1519 2.4 48.7 1.0 O C:HOH1352 2.6 25.6 1.0 HD22 C:ASN750 3.1 40.0 1.0 HA C:ALA749 3.2 31.1 1.0 HA C:SER746 3.3 34.3 1.0 C C:SER746 3.3 29.4 1.0 C C:MET748 3.3 26.2 1.0 H C:ASN750 3.7 31.8 1.0 HD21 C:ASN750 3.7 40.0 1.0 ND2 C:ASN750 3.7 33.4 1.0 CA C:SER746 3.8 28.6 1.0 N C:ALA749 4.0 26.6 1.0 CA C:ALA749 4.0 25.9 1.0 HB2 C:SER746 4.1 35.9 1.0 HZ1 A:LYS439 4.1 62.6 1.0 N C:MET748 4.2 29.8 1.0 O A:HOH1582 4.2 40.4 1.0 N C:LYS747 4.3 31.9 1.0 C C:LYS747 4.4 30.1 1.0 N C:ASN750 4.4 26.5 1.0 O C:LEU787 4.4 37.0 1.0 HE3 A:LYS439 4.4 62.2 1.0 H C:MET748 4.4 35.8 1.0 CA C:MET748 4.4 28.4 1.0 O C:VAL745 4.5 28.3 1.0 HA C:LYS747 4.5 38.5 1.0 CB C:SER746 4.5 29.9 1.0 HZ2 A:LYS439 4.6 62.6 1.0 O A:HOH1457 4.7 36.9 1.0 CA C:LYS747 4.7 32.1 1.0 O C:GLY788 4.7 24.3 1.0 NZ A:LYS439 4.7 52.2 1.0 O C:LYS747 4.8 29.8 1.0 C C:ALA749 4.8 25.9 1.0 H C:ALA749 4.8 31.9 1.0 O A:HOH1400 4.9 44.9 1.0 OD1 C:ASN789 4.9 31.3 1.0 HA3 C:GLY788 5.0 32.3 1.0 CG C:ASN750 5.0 32.4 1.0

S.Bodea, M.A.Funk, E.P.Balskus, C.L.Drennan. Molecular Basis of C-N Bond Cleavage By the Glycyl Radical Enzyme Choline Trimethylamine-Lyase. Cell Chem Biol V. 23 1206 2016.
ISSN: ESSN 2451-9456
PubMed: 27642068
DOI: 10.1016/J.CHEMBIOL.2016.07.020